[phenixbb] den refinement

Jeff Headd jjheadd at lbl.gov
Tue Jun 11 08:54:38 PDT 2013


Hi Andreas,

My guess is that you have main.simulated_annealing=True also active in your
parameter file. You need to set this to False, and then the refinement
should proceed.

Jeff


On Tue, Jun 11, 2013 at 11:44 AM, Andreas Förster <docandreas at gmail.com>wrote:

> Dear all,
>
> I'm trying to get DEN refinement going from the command line.  The run
> aborts quickly with the following error in the log file:
>
> Sorry: Cartesian simulated annealing should not be turned on for DEN
> refinement. Annealing settings are controlled in the den parameter scope.
>
> The DEN scope in input.def looks like this:
>
>   den {
>     reference_file = den_ref_Jun.pdb
>     gamma = 0.5
>     kappa = 0.1
>     weight = 30
>     sigma = 0.44
>     optimize = True
>     opt_gamma_values = 0 0.2 0.4 0.6 0.8 1
>     opt_weight_values = 3 10 30 100 300
>     num_cycles = 12
>     kappa_burn_in_cycles = 2
>     bulk_solvent_and_scale = True
>     refine_adp = True
>     final_refinement_cycle = False
>     verbose = False
>     annealing_type = *torsion cartesian
>     output_kinemage = False
>     restraint_network {
>       lower_distance_cutoff = 3
>       upper_distance_cutoff = 15
>       sequence_separation_low = 0
>       sequence_separation_limit = 10
>       exclude_hydrogens = True
>       ndistance_ratio = 1
>       export_den_pairs = False
>       den_network_file = None
>     }
>
> Annealing type is torsion from what I can tell.  What am I doing wrong?
>
> (Release tag: 1394, Platform: intel-linux-2.6-x86_64 redhat-e6.2)
>
>
> Thanks.
>
>
> Andreas
>
>
> --
>         Andreas Förster, Research Associate
>         Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>             http://www.msf.bio.ic.ac.uk
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